A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case

Simple item page
dc.contributor.authorYu, G. X.en
dc.contributor.authorSnyder, E. E.en
dc.contributor.authorBoyle, S. M.en
dc.contributor.authorCrasta, Oswald R.en
dc.contributor.authorCzar, M. J.en
dc.contributor.authorMane, S. P.en
dc.contributor.authorPurkayastha, A.en
dc.contributor.authorSobral, Brunoen
dc.contributor.authorSetubal, Joao C.en
dc.date.accessioned2019-04-19T18:32:02Zen
dc.date.available2019-04-19T18:32:02Zen
dc.date.issued2007-06en
dc.description.abstractWe present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity.en
dc.description.sponsorshipPHS HHS [HHSN266200400035C]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkm377en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issue12en
dc.identifier.pmid17553834en
dc.identifier.urihttp://hdl.handle.net/10919/89061en
dc.identifier.volume35en
dc.language.isoenen
dc.rightsCreative Commons Attribution-NonCommercial 2.0 Genericen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/en
dc.subjecturease-negative mutanten
dc.subjecthelicobacter-pylorien
dc.subjectiv secretionen
dc.subjectsuisen
dc.subjectmelitensisen
dc.subjectsequenceen
dc.subjectabortusen
dc.subjectproteinen
dc.subjectpurificationen
dc.subjectcolonizeen
dc.titleA versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use caseen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
gkm377.pdf
Size:
8 MB
Format:
Adobe Portable Document Format
Description:
Download

Collections

Scholarly Works, Fralin Life Sciences Institute
Scholarly Works, Virginia-Maryland College of Veterinary Medicine